Structures and kinetics of Thermotoga maritima MetY reveal new insights into the predominant sulfurylation enzyme of bacterial methionine biosynthesis

Abstract

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On the illusion of auxotrophy:met15Δyeast cells can grow on inorganic sulfur thanks to the previously uncharacterized homocysteine synthase Yll058w

“…For clarity, only the active site residues are shown. An O-acetyl-homoserine derivative reaction intermediate captured within the MetY structure (Brewster et al, 2021) is shown in semi-transparent spheres. Residue labeling corresponds to the Yll058w sequence.…”

“…The sequence similarity and evolutionary relationship of Yll058w to enzymes involved in sulfur metabolism led us to examine its predicted structure. To do so, we utilized the crystal structure of MetY ( Figure S7A ), a bacterial O -acetylhomoserine aminocarboxypropyltransferase that catalyzes the homocysteine biosynthesis from O -acetylhomoserine and bisulfide (Brewster et al ., 2021), as well as the predicted structures of Met15 and Yll058w generated by AlphaFold2 (Jumper et al, 2021). The MetY crystal structure captured a reaction intermediate, allowing for a precise determination of active site residues.…”

“…One difference is position 280 in the Yll058w sequence, which is a phenylalanine in Yll058w but a tyrosine in both Met15 and MetY. Another difference in the overall fold is that MetY and Met15 function as homotetramers (Brewster et al ., 2021; Yamagata, 1976), with multimerization domains allowing the distinct monomers to come together to complete the active site ( Figure S7C ). In contrast, Yll058w lacks a multimerization domain and is predicted to be monomeric.…”

“…Overlap of the active site residues of MetY from Thermatoga maritima (PDB ID: 7KB1) (gray) with the predicted structures of Yll058w (magenta) and Met15 (violet), calculated using AlphaFold, are shown. A reaction intermediate captured within the MetY structure (23) is shown in semitransparent spheres. Residue labeling corresponds to the Yll058w sequence.…”

“… A) A cartoon view of the MetY monomer, from the MetY crystal structure, pdbID:7KB1 (Brewster et al, 2021). The N-terminal tetramerization domain is shown in orange, the PLP-binding domain is shown in light purple, and the C-terminal substrate binding domain is shown in pale green.…”